Reef Structure and Physical Features: Atolls, barrier reefs, fringing reefs, patch reefs, and reef communities all occur in the Hawaiian Islands. Reef communities and fringing reefs are the dominate reef types found within the Hawaiian Islands Humpback Whale National Marine Sanctuary boundaries. The island of Hawai'i (the Big Island) has virtually no fringing reefs but some well developed reef communities and apron reefs occur off the Kona Coast (western coast).

Most of Kauai's coastline is bordered by fringing reefs. In many areas, reef flats are wide and extend more than 1 km from shore. Offshore, significant reefs are found around much of the island at 5 to 30 m depths. Small apron reefs dominated by crustose coralline algae extend from the coastline at Miloli'i and Nualolo-Kai.

Along much of Maui's north coast reefs are sparsely developed. This sparse development is common along unprotected areas of the north coasts of the islands due to the prevailing northeast winter swells and trade winds. The reefs are patchy and poorly formed. They are no more than thin veneers on outcrops of Pleistocene limestone or volcanics of various origin. Maui's southern and western shores are characterized by scattered fringing reefs and reef communities.

Fringing reefs are also found off the north and northeast coast of Lana'i Island, the south coast of Moloka'i Island, and around O'ahu Island, with the exception of its north and northwest coasts. Along the south side Moloka'i Island, the reef is well-developed with a width over 1 km in many places. This fringing reef is the longest in the state.

Coral Species and Cover: A total of 47 coral species are found in Hawaiian waters. Common species include: Porities lobata, P. compressa, Pavona varians, Montipora capitata, and Pocillopora meandrina. P. compressa and M. capitata are endemic.

The best developed reefs off the Big Island were assessed in the 1980s to have an average cover of about 67 percent.

Other fauna and flora: Humpback whales use the Hawaiian Islands Humpback Whale National Marine Sanctuary as their mating grounds. Hawaiian monk seal, other marine mammals, hawksbill and green sea turtles are found in the area. About 450 species of inshore fishes can be found in Hawaiian waters, of which approximately 25 percent are endemic. Approximately, 25 percent of sponges and 28 percent of polychaetes in the area are also endemic.